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GSR: Simulator - SIApopr
| Attribute | Value |
|---|---|
| Title | SIApopr |
| Short Description | Siapopr is an R package that wraps the C++ functions SIApop. These functions simulate birth-death-mutation processes with mutations having random fitnesses to simulate clonal evolution. |
| Long Description | Siapopr is an R package that wraps the C++ functions SIApop. These functions simulate birth-death-mutation processes with mutations having random fitnesses to simulate clonal evolution. |
| Version | Not available |
| Homepage | https://github.com/olliemcdonald/siapopr#readme |
| Citations | McDonald TO, Michor F, SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution., Bioinformatics, July 15, 2017 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | May 17, 2022 (1193 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | Single-locus, |
| Models | |
| Recombination | |
| Mutation Models | Infinite-allele Model, Others, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, R, Other, |
| License | Other, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used SIApopr.
2019
Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, et al., Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments., Nat Cell Biol, July 1, 2019 [Abstract]
2018
McDonald TO, Chakrabarti S, Michor F, Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution., Nat Genet, Dec. 1, 2018 [Abstract]
Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, et al., KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance., Cancer Cell, Dec. 10, 2018 [Abstract]